[gmx-users] pdb2gmx error

[Dries Van Rompaey]

Hi Mark,

This is Gromacs 5.0.4. This is a non-terminal residue.
The command line used is:
gmx pdb2gmx -f complex.pdb -o complex.gro (-ignh)
I tried this procedure with and without ignh flag.
As far as I know, specbonds is not in play.

Kind regards,
Dries


On 7 October 2015 at 20:56, Mark Abraham <mark.j.abraham at gmail.com> wrote:

> Hi,
>
> Is it terminal? Are there specbonds in play? What's the GROMACS version?
> What's your pdb2gmx command line? :-)
>
> Mark
>
> On Wed, Oct 7, 2015 at 8:43 PM Dries Van Rompaey <
> dries.vanrompaey at gmail.com>
> wrote:
>
> > Hi everyone,
> >
> > I'm getting the following warning when I try to run pdb2gmx on my protein
> > structure:
> >
> > WARNING: WARNING: Residue 168 named PRO of a molecule in the input file
> was
> > mapped to an entry in the topology database, but the atom H used in an
> > interaction of type dihedral in that entry is not found in the input
> file.
> > Perhaps your atom and/or residue naming needs to be fixed.
> >
> > This warning is only present when I use the AMBER03 forcefield, all other
> > forcefields seem to work fine. I have tried this with both a structure
> > without hydrogens as well as a structure with hydrogens added, both with
> > and without the -ignh flag. I tried looking at the amber03 database files
> > as well as the amber99sb-ildn database files (amber99sb-ildn works just
> > fine), but I could not find any reason why this particular residue would
> be
> > problematic. pdb2gmx does not find any problems with the other proline
> > residues in the protein (which look identical), so I am puzzled as to
> > what's causing this.
> >
> > The proline residue is:
> > ATOM   1384  N   PRO A 168     274.650  45.241  24.167  1.00180.63
> >   N
> > ATOM   1385  CA  PRO A 168     273.508  44.823  23.370  1.00180.63
> >   C
> > ATOM   1386  CD  PRO A 168     275.844  45.381  23.346  1.00180.63
> >   C
> > ATOM   1387  CB  PRO A 168     274.071  44.405  22.014  1.00180.63
> >   C
> > ATOM   1388  CG  PRO A 168     275.381  45.194  21.892  1.00180.63
> >   C
> > ATOM   1389  C   PRO A 168     272.551  43.776  23.888  1.00180.63
> >   C
> > ATOM   1390  O   PRO A 168     271.478  43.646  23.304  1.00180.63
> >   O
> >
> > Does anyone know what's going on here?
> >
> > Thanks in advance!
> > --
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